All eukaryotic chromosomes have a centromere, which ensures that the genomic DNA is shared equally between daughter cells during cell division. Centromeres are defined by the presence of nucleosomes that contain a special histone H3 variant, CenH3. Accumulating evidence suggests that CenH3-containing nucleosomes have an unusual structure: Rather than consisting of the highly conserved octamer of histone proteins, which wraps up ∼147 bp of DNA, they may instead form tetramers, which wrap only half as much DNA.

To understand how widespread this unusual centromeric nucleosome conformation might be, Krassovsky et al. fine-map the positions of budding yeast centromeres, which consist of a single CenH3 (known as Cse4) nucleosome binding site on each chromosome. Cse4 binds a region of DNA that is 80 bp in length, consistent with a tetramer nucleosome conformation. The highly AT-rich DNA sequence at the centromere and two protein-binding sites that flank the centromere site probably exclude binding of the canonical octamer nucleosome and recruit and stabilize the binding of the Cse4 nucleosome. Cse4 nucleosomes that become misincorporated at noncentromere sites, on the other hand, form octamers and are found in regions of high nucleosome turnover, the latter observation hinting how such excess Cse4, which could impede the function of the centromere, might be purged from the genome.